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1. DESI 2024 VII: Cosmological Constraints from the Full-Shape Modeling of Clustering Measurements

Author: DESI Collaboration, Adame, A. G., Aguilar, J., Ahlen, S., Alam, S., Alexander, D. M., Prieto, C. Allende, Alvarez, M., Alves, O., Anand, A., Andrade, U., Armengaud, E., Avila, S., Aviles, A., Awan, H., Bahr-Kalus, B., Bailey, S., Baltay, C., Bault, A., Behera, J., BenZvi, S., Beutler, F., Bianchi, D., Blake, C., Blum, R., Bonici, M., Brieden, S., Brodzeller, A., Brooks, D., Buckley-Geer, E., Burtin, E., Calderon, R., Canning, R., Rosell, A. Carnero, Cereskaite, R., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chaves-Montero, J., Chebat, D., Chen, S., Chen, X., Claybaugh, T., Cole, S., Cuceu, A., Davis, T. M., Dawson, K., de la Macorra, A., de Mattia, A., Deiosso, N., Dey, A., Dey, B., Ding, Z., Doel, P., Edelstein, J., Eftekharzadeh, S., Eisenstein, D. J., Elbers, W., Elliott, A., Fagrelius, P., Fanning, K., Ferraro, S., Ereza, J., Findlay, N., Flaugher, B., Font-Ribera, A., Forero-Sánchez, D., Forero-Romero, J. E., Frenk, C. S., Garcia-Quintero, C., Garrison, L. H., Gaztañaga, E., Gil-Marín, H., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Gonzalez-Perez, V., Gordon, C., Green, D., Gruen, D., Gsponer, R., Gutierrez, G., Guy, J., Hadzhiyska, B., Hahn, C., Hanif, M. M. S, Herrera-Alcantar, H. K., Honscheid, K., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Joyce, R., Juneau, S., Karaçaylı, N. G., Kehoe, R., Kent, S., Kirkby, D., Kong, H., Koposov, S. E., Kremin, A., Krolewski, A., Lahav, O., Lai, Y., Lan, T. -W., Landriau, M., Lang, D., Lasker, J., Goff, J. M. Le, Guillou, L. Le, Leauthaud, A., Levi, M. E., Li, T. S., Lodha, K., Magneville, C., Manera, M., Margala, D., Martini, P., Matthewson, W., Maus, M., McDonald, P., Medina-Varela, L., Meisner, A., Mena-Fernández, J., Miquel, R., Moon, J., Moore, S., Moustakas, J., Mudur, N., Mueller, E., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Napolitano, L., Neveux, R., Newman, J. A., Nguyen, N. M., Nie, J., Niz, G., Noriega, H. E., Padmanabhan, N., Paillas, E., Palanque-Delabrouille, N., Pan, J., Penmetsa, S., Percival, W. J., Pieri, M. M., Pinon, M., Poppett, C., Porredon, A., Prada, F., Pérez-Fernández, A., Pérez-Ràfols, I., Rabinowitz, D., Raichoor, A., Ramírez-Pérez, C., Ramirez-Solano, S., Rashkovetskyi, M., Ravoux, C., Rezaie, M., Rich, J., Rocher, A., Rockosi, C., Roe, N. A., Rosado-Marin, A., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Samushia, L., Sanchez, E., Saulder, C., Schlafly, E. F., Schlegel, D., Schubnell, M., Seo, H., Shafieloo, A., Sharples, R., Silber, J., Slosar, A., Smith, A., Sprayberry, D., Tan, T., Tarlé, G., Taylor, P., Trusov, S., Vaisakh, R., Valcin, D., Valdes, F., Valogiannis, G., Vargas-Magaña, M., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, N., Wechsler, R. H., Weinberg, D. H., White, M., Wilson, M. J., Yi, L., Yu, J., Yu, Y., Yuan, S., Yèche, C., Zaborowski, E. A., Zarrouk, P., Zhang, H., Zhao, C., Zhao, R., Zhou, R., Zhuang, T., and Zou, H.
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract: We present cosmological results from the measurement of clustering of galaxy, quasar and Lyman-$\alpha$ forest tracers from the first year of observations with the Dark Energy Spectroscopic Instrument (DESI Data Release 1). We adopt the full-shape (FS) modeling of the power spectrum, including the effects of redshift-space distortions, in an analysis which has been validated in a series of supporting papers. In the flat $\Lambda$CDM cosmological model, DESI (FS+BAO), combined with a baryon density prior from Big Bang Nucleosynthesis and a weak prior on the scalar spectral index, determines matter density to $\Omega_\mathrm{m}=0.2962\pm 0.0095$, and the amplitude of mass fluctuations to $\sigma_8=0.842\pm 0.034$. The addition of the cosmic microwave background (CMB) data tightens these constraints to $\Omega_\mathrm{m}=0.3056\pm 0.0049$ and $\sigma_8=0.8121\pm 0.0053$, while further addition of the the joint clustering and lensing analysis from the Dark Energy Survey Year-3 (DESY3) data leads to a 0.4% determination of the Hubble constant, $H_0 = (68.40\pm 0.27)\,{\rm km\,s^{-1}\,Mpc^{-1}}$. In models with a time-varying dark energy equation of state, combinations of DESI (FS+BAO) with CMB and type Ia supernovae continue to show the preference, previously found in the DESI DR1 BAO analysis, for $w_0>-1$ and $w_a<0$ with similar levels of significance. DESI data, in combination with the CMB, impose the upper limits on the sum of the neutrino masses of $\sum m_\nu < 0.071\,{\rm eV}$ at 95% confidence. DESI data alone measure the modified-gravity parameter that controls the clustering of massive particles, $\mu_0=0.11^{+0.45}_{-0.54}$, while the combination of DESI with the CMB and the clustering and lensing analysis from DESY3 constrains both modified-gravity parameters, giving $\mu_0 = 0.04\pm 0.22$ and $\Sigma_0 = 0.044\pm 0.047$, in agreement with general relativity. [Abridged.], Comment: This DESI Collaboration Key Publication is part of the 2024 publication series using the first year of observations (see https://data.desi.lbl.gov/doc/papers/). 55 pages, 10 figures
Published: 2024

2. DESI 2024 II: Sample Definitions, Characteristics, and Two-point Clustering Statistics

Author: DESI Collaboration, Adame, A. G., Aguilar, J., Ahlen, S., Alam, S., Alexander, D. M., Alvarez, M., Alves, O., Anand, A., Andrade, U., Armengaud, E., Avila, S., Aviles, A., Awan, H., Bailey, S., Baltay, C., Bault, A., Behera, J., BenZvi, S., Beutler, F., Bianchi, D., Blake, C., Blum, R., Brieden, S., Brodzeller, A., Brooks, D., Brown, Z., Buckley-Geer, E., Burtin, E., Calderon, R., Canning, R., Rosell, A. Carnero, Cereskaite, R., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chaves-Montero, J., Chen, S., Chen, X., Claybaugh, T., Cole, S., Cuceu, A., Davis, T. M., Dawson, K., de la Macorra, A., de Mattia, A., Deiosso, N., Demina, R., Dey, A., Dey, B., Ding, Z., Doel, P., Edelstein, J., Eftekharzadeh, S., Eisenstein, D. J., Elliott, A., Fagrelius, P., Fanning, K., Ferraro, S., Ereza, J., Findlay, N., Flaugher, B., Font-Ribera, A., Forero-Sánchez, D., Forero-Romero, J. E., Frenk, C. S., Garcia-Quintero, C., Gaztañaga, E., Gil-Marín, H., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Gonzalez-Perez, V., Gordon, C., Green, D., Gruen, D., Gsponer, R., Gutierrez, G., Guy, J., Hadzhiyska, B., Hahn, C., Hanif, M. M. S, Herrera-Alcantar, H. K., Honscheid, K., Hou, J., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Juneau, S., Karaçaylı, N. G., Kehoe, R., Kent, S., Kirkby, D., Kitaura, F. -S., Kong, H., Kremin, A., Krolewski, A., Lai, Y., Lan, T. -W., Landriau, M., Lang, D., Lasker, J., Goff, J. M. Le, Guillou, L. Le, Leauthaud, A., Levi, M. E., Li, T. S., Lodha, K., Magneville, C., Manera, M., Margala, D., Martini, P., Maus, M., McDonald, P., Medina-Varela, L., Meisner, A., Mena-Fernández, J., Miquel, R., Moon, J., Moore, S., Moustakas, J., Mudur, N., Mueller, E., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Napolitano, L., Neveux, R., Newman, J. A., Nguyen, N. M., Nie, J., Niz, G., Noriega, H. E., Padmanabhan, N., Paillas, E., Palanque-Delabrouille, N., Pan, J., Penmetsa, S., Percival, W. J., Pieri, M. M., Pinon, M., Poppett, C., Porredon, A., Prada, F., Pérez-Fernández, A., Pérez-Ràfols, I., Rabinowitz, D., Raichoor, A., Ramírez-Pérez, C., Ramirez-Solano, S., Rashkovetskyi, M., Ravoux, C., Rezaie, M., Rich, J., Rocher, A., Rockosi, C., Roe, N. A., Rosado-Marin, A., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Samushia, L., Sanchez, E., Saulder, C., Schlafly, E. F., Schlegel, D., Scholte, D., Schubnell, M., Seo, H., Sharples, R., Silber, J., Slosar, A., Smith, A., Sprayberry, D., Tan, T., Tarlé, G., Trusov, S., Vaisakh, R., Valcin, D., Valdes, F., Vargas-Magaña, M., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, N., Wechsler, R. H., Weinberg, D. H., White, M., Wilson, M. J., Yu, J., Yu, Y., Yuan, S., Yèche, C., Zaborowski, E. A., Zarrouk, P., Zhang, H., Zhao, C., Zhao, R., Zhou, R., and Zou, H.
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract: We present the samples of galaxies and quasars used for DESI 2024 cosmological analyses, drawn from the DESI Data Release 1 (DR1). We describe the construction of large-scale structure (LSS) catalogs from these samples, which include matched sets of synthetic reference `randoms' and weights that account for variations in the observed density of the samples due to experimental design and varying instrument performance. We detail how we correct for variations in observational completeness, the input `target' densities due to imaging systematics, and the ability to confidently measure redshifts from DESI spectra. We then summarize how remaining uncertainties in the corrections can be translated to systematic uncertainties for particular analyses. We describe the weights added to maximize the signal-to-noise of DESI DR1 2-point clustering measurements. We detail measurement pipelines applied to the LSS catalogs that obtain 2-point clustering measurements in configuration and Fourier space. The resulting 2-point measurements depend on window functions and normalization constraints particular to each sample, and we present the corrections required to match models to the data. We compare the configuration- and Fourier-space 2-point clustering of the data samples to that recovered from simulations of DESI DR1 and find they are, generally, in statistical agreement to within 2\% in the inferred real-space over-density field. The LSS catalogs, 2-point measurements, and their covariance matrices will be released publicly with DESI DR1., Comment: This DESI Collaboration Key Publication is part of the 2024 publication series using the first year of observations (see https://data.desi.lbl.gov/doc/papers/)
Published: 2024

3. DESI 2024 V: Full-Shape Galaxy Clustering from Galaxies and Quasars

Author: DESI Collaboration, Adame, A. G., Aguilar, J., Ahlen, S., Alam, S., Alexander, D. M., Alvarez, M., Alves, O., Anand, A., Andrade, U., Armengaud, E., Avila, S., Aviles, A., Awan, H., Bailey, S., Baltay, C., Bault, A., Behera, J., BenZvi, S., Beutler, F., Bianchi, D., Blake, C., Blum, R., Brieden, S., Brodzeller, A., Brooks, D., Buckley-Geer, E., Burtin, E., Calderon, R., Canning, R., Rosell, A. Carnero, Cereskaite, R., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chaves-Montero, J., Chen, S., Chen, X., Claybaugh, T., Cole, S., Cuceu, A., Davis, T. M., Dawson, K., de la Macorra, A., de Mattia, A., Deiosso, N., Dey, A., Dey, B., Ding, Z., Doel, P., Edelstein, J., Eftekharzadeh, S., Eisenstein, D. J., Elliott, A., Fagrelius, P., Fanning, K., Ferraro, S., Ereza, J., Findlay, N., Flaugher, B., Font-Ribera, A., Forero-Sánchez, D., Forero-Romero, J. E., Garcia-Quintero, C., Garrison, L. H., Gaztañaga, E., Gil-Marín, H., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Gonzalez-Perez, V., Gordon, C., Green, D., Gruen, D., Gsponer, R., Gutierrez, G., Guy, J., Hadzhiyska, B., Hahn, C., Hanif, M. M. S, Herrera-Alcantar, H. K., Honscheid, K., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Juneau, S., Karaçaylı, N. G., Kehoe, R., Kent, S., Kirkby, D., Kong, H., Koposov, S. E., Kremin, A., Krolewski, A., Lai, Y., Lan, T. -W., Landriau, M., Lang, D., Lasker, J., Goff, J. M. Le, Guillou, L. Le, Leauthaud, A., Levi, M. E., Li, T. S., Lodha, K., Magneville, C., Manera, M., Margala, D., Martini, P., Maus, M., McDonald, P., Medina-Varela, L., Meisner, A., Mena-Fernández, J., Miquel, R., Moon, J., Moore, S., Moustakas, J., Mueller, E., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Napolitano, L., Neveux, R., Newman, J. A., Nguyen, N. M., Nie, J., Niz, G., Noriega, H. E., Padmanabhan, N., Paillas, E., Palanque-Delabrouille, N., Pan, J., Penmetsa, S., Percival, W. J., Pieri, M. M., Pinon, M., Poppett, C., Porredon, A., Prada, F., Pérez-Fernández, A., Pérez-Ràfols, I., Rabinowitz, D., Raichoor, A., Ramírez-Pérez, C., Ramirez-Solano, S., Rashkovetskyi, M., Ravoux, C., Rezaie, M., Rich, J., Rocher, A., Rockosi, C., Rodríguez-Martínez, F., Roe, N. A., Rosado-Marin, A., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Samushia, L., Sanchez, E., Saulder, C., Schlafly, E. F., Schlegel, D., Schubnell, M., Seo, H., Sharples, R., Silber, J., Slosar, A., Smith, A., Sprayberry, D., Tan, T., Tarlé, G., Trusov, S., Vaisakh, R., Valcin, D., Valdes, F., Vargas-Magaña, M., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, N., Wechsler, R. H., Weinberg, D. H., White, M., Wilson, M. J., Yu, J., Yu, Y., Yuan, S., Yèche, C., Zaborowski, E. A., Zarrouk, P., Zhang, H., Zhao, C., Zhao, R., Zhou, R., and Zou, H.
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract: We present the measurements and cosmological implications of the galaxy two-point clustering using over 4.7 million unique galaxy and quasar redshifts in the range $0.1
Published: 2024

4. Identifying the Mechanisms of Water Maser Variability During the Accretion Burst in NGC6334I

Author: Vorster, Jakobus M., Chibueze, James O., Hirota, Tomoya, MacLeod, Gordon C., van der Walt, Johan D., Vorobyov, Eduard I., Sobolev, Andrej M., and Juvela, Mika
Subjects: Astrophysics - Astrophysics of Galaxies, Astrophysics - Solar and Stellar Astrophysics
Abstract: HMYSOs gain most of their mass in short bursts of accretion. Maser emission is an invaluable tool in discovering and probing accretion bursts. We observed the 22 GHz water maser response induced by the accretion burst in NGC6334I-MM1B and identified the underlying maser variability mechanisms. We report seven epochs of VLBI observations of 22 GHz water masers in NGC6334I with the VERA array, from 2014 to 2016, spanning the onset of the accretion burst in 2015.1. We also report 2019 ALMA observations of 321 GHz water masers and 22 GHz maser monitoring by HartRAO. We analyze variability patterns and use proper motions with the 22 GHz to 321 GHz line ratio to distinguish between masers in C-shocks and J-shocks. We also calculated the burst-to-quiescent variance ratio of the single-dish time series. The constant mean proper motion before and after the burst indicates that maser variability is due to excitation effects from variable radiation rather than jet ejecta. We find that the flux density variance ratio in the single-dish time series can identify maser efficiency variations in 22 GHz masers. The northern region, CM2-W2, is excited in C-shocks and showed long-term flaring with velocity-dependent excitation of new maser features. We propose that radiative heating of H2 due to high-energy radiation from the accretion burst be the mechanism for the flaring in CM2-W2. The southern regions are excited by J-shocks and have short-term flaring and dampening of water masers. We attributed the diverse variability patterns in the southern regions to the radiative transfer of the burst energy in the source. Our results indicate that the effects of source geometry, shock type, and incident radiation spectrum are fundamental factors affecting 22 GHz maser variability. Investigating water masers in irradiated shocks will improve their use as a diagnostic in time-variable radiation environments., Comment: 21 pages, 12 figures, Table 2 in electronic publication. Contact: jakobus.vorster@helsinki.fi
Published: 2024
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5. DESI 2024 VI: Cosmological Constraints from the Measurements of Baryon Acoustic Oscillations

Author: DESI Collaboration, Adame, A. G., Aguilar, J., Ahlen, S., Alam, S., Alexander, D. M., Alvarez, M., Alves, O., Anand, A., Andrade, U., Armengaud, E., Avila, S., Aviles, A., Awan, H., Bahr-Kalus, B., Bailey, S., Baltay, C., Bault, A., Behera, J., BenZvi, S., Bera, A., Beutler, F., Bianchi, D., Blake, C., Blum, R., Brieden, S., Brodzeller, A., Brooks, D., Buckley-Geer, E., Burtin, E., Calderon, R., Canning, R., Rosell, A. Carnero, Cereskaite, R., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chaves-Montero, J., Chen, S., Chen, X., Claybaugh, T., Cole, S., Cuceu, A., Davis, T. M., Dawson, K., de la Macorra, A., de Mattia, A., Deiosso, N., Dey, A., Dey, B., Ding, Z., Doel, P., Edelstein, J., Eftekharzadeh, S., Eisenstein, D. J., Elliott, A., Fagrelius, P., Fanning, K., Ferraro, S., Ereza, J., Findlay, N., Flaugher, B., Font-Ribera, A., Forero-Sánchez, D., Forero-Romero, J. E., Frenk, C. S., Garcia-Quintero, C., Gaztañaga, E., Gil-Marín, H., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Gonzalez-Perez, V., Gordon, C., Green, D., Gruen, D., Gsponer, R., Gutierrez, G., Guy, J., Hadzhiyska, B., Hahn, C., Hanif, M. M. S, Herrera-Alcantar, H. K., Honscheid, K., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Juneau, S., Karaçaylı, N. G., Kehoe, R., Kent, S., Kirkby, D., Kremin, A., Krolewski, A., Lai, Y., Lan, T. -W., Landriau, M., Lang, D., Lasker, J., Goff, J. M. Le, Guillou, L. Le, Leauthaud, A., Levi, M. E., Li, T. S., Linder, E., Lodha, K., Magneville, C., Manera, M., Margala, D., Martini, P., Maus, M., McDonald, P., Medina-Varela, L., Meisner, A., Mena-Fernández, J., Miquel, R., Moon, J., Moore, S., Moustakas, J., Mudur, N., Mueller, E., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Napolitano, L., Neveux, R., Newman, J. A., Nguyen, N. M., Nie, J., Niz, G., Noriega, H. E., Padmanabhan, N., Paillas, E., Palanque-Delabrouille, N., Pan, J., Penmetsa, S., Percival, W. J., Pieri, M. M., Pinon, M., Poppett, C., Porredon, A., Prada, F., Pérez-Fernández, A., Pérez-Ràfols, I., Rabinowitz, D., Raichoor, A., Ramírez-Pérez, C., Ramirez-Solano, S., Ravoux, C., Rashkovetskyi, M., Rezaie, M., Rich, J., Rocher, A., Rockosi, C., Roe, N. A., Rosado-Marin, A., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Samushia, L., Sanchez, E., Saulder, C., Schlafly, E. F., Schlegel, D., Schubnell, M., Seo, H., Shafieloo, A., Sharples, R., Silber, J., Slosar, A., Smith, A., Sprayberry, D., Tan, T., Tarlé, G., Taylor, P., Trusov, S., Ureña-López, L. A., Vaisakh, R., Valcin, D., Valdes, F., Vargas-Magaña, M., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, N., Wechsler, R. H., Weinberg, D. H., White, M., Yu, J., Yu, Y., Yuan, S., Yèche, C., Zaborowski, E. A., Zarrouk, P., Zhang, H., Zhao, C., Zhao, R., Zhou, R., Zhuang, T., and Zou, H.
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract: We present cosmological results from the measurement of baryon acoustic oscillations (BAO) in galaxy, quasar and Lyman-$\alpha$ forest tracers from the first year of observations from the Dark Energy Spectroscopic Instrument (DESI), to be released in the DESI Data Release 1. DESI BAO provide robust measurements of the transverse comoving distance and Hubble rate, or their combination, relative to the sound horizon, in seven redshift bins from over 6 million extragalactic objects in the redshift range $0.1-1$ and $w_a<0$. This preference is 2.6$\sigma$ for the DESI+CMB combination, and persists or grows when SN~Ia are added in, giving results discrepant with the $\Lambda$CDM model at the $2.5\sigma$, $3.5\sigma$ or $3.9\sigma$ levels for the addition of Pantheon+, Union3, or DES-SN5YR datasets respectively. For the flat $\Lambda$CDM model with the sum of neutrino mass $\sum m_\nu$ free, combining the DESI and CMB data yields an upper limit $\sum m_\nu < 0.072$ $(0.113)$ eV at 95% confidence for a $\sum m_\nu>0$ $(\sum m_\nu>0.059)$ eV prior. These neutrino-mass constraints are substantially relaxed in models beyond $\Lambda$CDM. [Abridged.], Comment: This DESI Collaboration Key Publication is part of the 2024 publication series using the first year of observations (see https://data.desi.lbl.gov/doc/papers). 68 pages, 15 figures. Version accepted for publication in JCAP
Published: 2024

6. DESI 2024 IV: Baryon Acoustic Oscillations from the Lyman Alpha Forest

Author: DESI Collaboration, Adame, A. G., Aguilar, J., Ahlen, S., Alam, S., Alexander, D. M., Alvarez, M., Alves, O., Anand, A., Andrade, U., Armengaud, E., Avila, S., Aviles, A., Awan, H., Bailey, S., Baltay, C., Bault, A., Bautista, J., Behera, J., BenZvi, S., Beutler, F., Bianchi, D., Blake, C., Blum, R., Brieden, S., Brodzeller, A., Brooks, D., Buckley-Geer, E., Burtin, E., Calderon, R., Canning, R., Rosell, A. Carnero, Cereskaite, R., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chaves-Montero, J., Chen, S., Chen, X., Claybaugh, T., Cole, S., Cuceu, A., Davis, T. M., Dawson, K., de la Cruz, R., de la Macorra, A., de Mattia, A., Deiosso, N., Dey, A., Dey, B., Ding, J., Ding, Z., Doel, P., Edelstein, J., Eftekharzadeh, S., Eisenstein, D. J., Elliott, A., Fagrelius, P., Fanning, K., Ferraro, S., Ereza, J., Findlay, N., Flaugher, B., Font-Ribera, A., Forero-Sánchez, D., Forero-Romero, J. E., Garcia-Quintero, C., Gaztañaga, E., Gil-Marín, H., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Gonzalez-Perez, V., Gordon, C., Green, D., Gruen, D., Gsponer, R., Gutierrez, G., Guy, J., Hadzhiyska, B., Hahn, C., Hanif, M. M. S, Herrera-Alcantar, H. K., Honscheid, K., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Juneau, S., Karaçayli, N. G., Kehoe, R., Kent, S., Kirkby, D., Kremin, A., Krolewski, A., Lai, Y., Lan, T. -W., Landriau, M., Lang, D., Lasker, J., Goff, J. M. Le, Guillou, L. Le, Leauthaud, A., Levi, M. E., Li, T. S., Linder, E., Lodha, K., Magneville, C., Manera, M., Margala, D., Martini, P., Maus, M., McDonald, P., Medina-Varela, L., Meisner, A., Mena-Fernández, J., Miquel, R., Moon, J., Moore, S., Moustakas, J., Mueller, E., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Napolitano, L., Neveux, R., Newman, J. A., Nguyen, N. M., Nie, J., Niz, G., Noriega, H. E., Padmanabhan, N., Paillas, E., Palanque-Delabrouille, N., Pan, J., Penmetsa, S., Percival, W. J., Pieri, M. M., Pinon, M., Poppett, C., Porredon, A., Prada, F., Pérez-Fernández, A., Pérez-Ràfols, I., Rabinowitz, D., Raichoor, A., Ramírez-Pérez, C., Ramirez-Solano, S., Rashkovetskyi, M., Ravoux, C., Rezaie, M., Rich, J., Rocher, A., Rockosi, C., Roe, N. A., Rosado-Marin, A., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Samushia, L., Sanchez, E., Saulder, C., Schlafly, E. F., Schlegel, D., Schubnell, M., Seo, H., Sharples, R., Silber, J., Sinigaglia, F., Slosar, A., Smith, A., Sprayberry, D., Tan, T., Tarlé, G., Trusov, S., Vaisakh, R., Valcin, D., Valdes, F., Vargas-Magaña, M., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, N., Wechsler, R. H., Weinberg, D. H., White, M., Yu, J., Yu, Y., Yuan, S., Yèche, C., Zaborowski, E. A., Zarrouk, P., Zhang, H., Zhao, C., Zhao, R., Zhou, R., and Zou, H.
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract: We present the measurement of Baryon Acoustic Oscillations (BAO) from the Lyman-$\alpha$ (Ly$\alpha$) forest of high-redshift quasars with the first-year dataset of the Dark Energy Spectroscopic Instrument (DESI). Our analysis uses over $420\,000$ Ly$\alpha$ forest spectra and their correlation with the spatial distribution of more than $700\,000$ quasars. An essential facet of this work is the development of a new analysis methodology on a blinded dataset. We conducted rigorous tests using synthetic data to ensure the reliability of our methodology and findings before unblinding. Additionally, we conducted multiple data splits to assess the consistency of the results and scrutinized various analysis approaches to confirm their robustness. For a given value of the sound horizon ($r_d$), we measure the expansion at $z_{\rm eff}=2.33$ with 2\% precision, $H(z_{\rm eff}) = (239.2 \pm 4.8) (147.09~{\rm Mpc} /r_d)$ km/s/Mpc. Similarly, we present a 2.4\% measurement of the transverse comoving distance to the same redshift, $D_M(z_{\rm eff}) = (5.84 \pm 0.14) (r_d/147.09~{\rm Mpc})$ Gpc. Together with other DESI BAO measurements at lower redshifts, these results are used in a companion paper to constrain cosmological parameters., Comment: This DESI Collaboration Key Publication is part of the 2024 publication series using the first year of observations (see https://data.desi.lbl.gov/doc/papers). Minor changes in v4, version accepted for publication in JCAP
Published: 2024

7. DESI 2024 III: Baryon Acoustic Oscillations from Galaxies and Quasars

Author: DESI Collaboration, Adame, A. G., Aguilar, J., Ahlen, S., Alam, S., Alexander, D. M., Alvarez, M., Alves, O., Anand, A., Andrade, U., Armengaud, E., Avila, S., Aviles, A., Awan, H., Bailey, S., Baltay, C., Bault, A., Behera, J., BenZvi, S., Beutler, F., Bianchi, D., Blake, C., Blum, R., Brieden, S., Brodzeller, A., Brooks, D., Buckley-Geer, E., Burtin, E., Calderon, R., Canning, R., Rosell, A. Carnero, Cereskaite, R., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chaves-Montero, J., Chen, S., Chen, X., Claybaugh, T., Cole, S., Cuceu, A., Davis, T. M., Dawson, K., de la Macorra, A., de Mattia, A., Deiosso, N., Dey, A., Dey, B., Ding, Z., Doel, P., Edelstein, J., Eftekharzadeh, S., Eisenstein, D. J., Elliott, A., Fagrelius, P., Fanning, K., Ferraro, S., Ereza, J., Findlay, N., Flaugher, B., Font-Ribera, A., Forero-Sánchez, D., Forero-Romero, J. E., Garcia-Quintero, C., Gaztañaga, E., Gil-Marín, H., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Gonzalez-Perez, V., Gordon, C., Green, D., Gruen, D., Gsponer, R., Gutierrez, G., Guy, J., Hadzhiyska, B., Hahn, C., Hanif, M. M. S, Herrera-Alcantar, H. K., Honscheid, K., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Juneau, S., Karaçaylı, N. G., Kehoe, R., Kent, S., Kirkby, D., Kremin, A., Krolewski, A., Lai, Y., Lan, T. -W., Landriau, M., Lang, D., Lasker, J., Goff, J. M. Le, Guillou, L. Le, Leauthaud, A., Levi, M. E., Li, T. S., Linder, E., Lodha, K., Magneville, C., Manera, M., Margala, D., Martini, P., Maus, M., McDonald, P., Medina-Varela, L., Meisner, A., Mena-Fernández, J., Miquel, R., Moon, J., Moore, S., Moustakas, J., Mudur, N., Mueller, E., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Napolitano, L., Neveux, R., Newman, J. A., Nguyen, N. M., Nie, J., Niz, G., Noriega, H. E., Padmanabhan, N., Paillas, E., Palanque-Delabrouille, N., Pan, J., Penmetsa, S., Percival, W. J., Pieri, M., Pinon, M., Poppett, C., Porredon, A., Prada, F., Pérez-Fernández, A., Pérez-Ràfols, I., Rabinowitz, D., Raichoor, A., Ramírez-Pérez, C., Ramirez-Solano, S., Rashkovetskyi, M., Rezaie, M., Rich, J., Rocher, A., Rockosi, C., Roe, N. A., Rosado-Marin, A., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Samushia, L., Sanchez, E., Saulder, C., Schlafly, E. F., Schlegel, D., Schubnell, M., Seo, H., Sharples, R., Silber, J., Slosar, A., Smith, A., Sprayberry, D., Swanson, J., Tan, T., Tarlé, G., Trusov, S., Vaisakh, R., Valcin, D., Valdes, F., Vargas-Magaña, M., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, N., Wechsler, R. H., Weinberg, D. H., White, M., Yu, J., Yu, Y., Yuan, S., Yèche, C., Zaborowski, E. A., Zarrouk, P., Zhang, H., Zhao, C., Zhao, R., Zhou, R., and Zou, H.
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract: We present the DESI 2024 galaxy and quasar baryon acoustic oscillations (BAO) measurements using over 5.7 million unique galaxy and quasar redshifts in the range 0.1
Published: 2024

8. Germline BRCA1/2 status and chemotherapy response score in high-grade serous ovarian cancer

Author: Morgan, Robert D., Wang, Xin, Barnes, Bethany M., Spurgeon, Laura, Carrot, Aurore, Netto, Daniel, Hasan, Jurjees, Mitchell, Claire, Salih, Zena, Desai, Sudha, Shaw, Joseph, Winter-Roach, Brett, Schlecht, Helene, Burghel, George J., Clamp, Andrew R., Edmondson, Richard J., You, Benoit, Evans, D. Gareth R., Jayson, Gordon C., and Taylor, Stephen S.
Published: 2024
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9. Impact of Systematic Redshift Errors on the Cross-correlation of the Lyman-$\alpha$ Forest with Quasars at Small Scales Using DESI Early Data

Author: Bault, Abby, Kirkby, David, Guy, Julien, Brodzeller, Allyson, Aguilar, J., Ahlen, S., Bailey, S., Brooks, D., Cabayol-Garcia, L., Chaves-Montero, J., Claybaugh, T., Cuceu, A., Dawson, K., de la Cruz, R., de la Macorra, A., Dey, A., Doel, P., Filbert, S., Font-Ribera, A., Forero-Romero, J. E., Gaztañaga, E., Gontcho, S. Gontcho A, Gordon, C., Herrera-Alcantar, H. K., Honscheid, K., Iršič, V., Karaçaylı, N. G., Kehoe, R., Kisner, T., Kremin, A., Lambert, A., Landriau, M., Guillou, L. Le, Levi, M. E., Manera, M., Martini, P., Meisner, A., Miquel, R., Montero-Camacho, P., Moustakas, J., Muñoz-Gutiérrez, A., Nie, J., Niz, G., Palanque-Delabrouille, N., Percival, W. J., Poppett, C., Prada, F., Pérez-Ràfols, I., Ramírez-Pérez, C., Ravoux, C., Rezaie, M., Rossi, G., Sanchez, E., Schlafly, E. F., Schlegel, D., Schubnell, M., Silber, J., Tan, T., Tarlé, G., Walther, M., Weaver, B. A., and Zhou, Z.
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract: The Dark Energy Spectroscopic Instrument (DESI) will measure millions of quasar spectra by the end of its 5 year survey. Quasar redshift errors impact the shape of the Lyman-$\alpha$ forest correlation functions, which can affect cosmological analyses and therefore cosmological interpretations. Using data from the DESI Early Data Release and the first two months of the main survey, we measure the systematic redshift error from an offset in the cross-correlation of the Lyman-$\alpha$ forest with quasars. We find evidence for a redshift dependent bias causing redshifts to be underestimated with increasing redshift, stemming from improper modeling of the Lyman-$\alpha$ optical depth in the templates used for redshift estimation. New templates were derived for the DESI Year 1 quasar sample at $z > 1.6$ and we found the redshift dependent bias, $\Delta r_\parallel$, increased from $-1.94 \pm 0.15$ $h^{-1}$ Mpc to $-0.08 \pm 0.04$ $h^{-1}$ Mpc ($-205 \pm 15~\text{km s}^{-1}$ to $-9.0 \pm 4.0~\text{km s}^{-1}$). These new templates will be used to provide redshifts for the DESI Year 1 quasar sample., Comment: 29 pages, 9 figures, 5 tables
Published: 2024

10. Synthetic spectra for Lyman-$\alpha$ forest analysis in the Dark Energy Spectroscopic Instrument

Author: Herrera-Alcantar, Hiram K., Muñoz-Gutiérrez, Andrea, Tan, Ting, González-Morales, Alma X., Font-Ribera, Andreu, Guy, Julien, Moustakas, John, Kirkby, David, Armengaud, E., Bault, A., Cabayol-Garcia, L., Chaves-Montero, J., Cuceu, A., de la Cruz, R., García, L. Á., Gordon, C., Iršič, V., Karaçaylı, N. G., Goff, J. M. Le, Montero-Camacho, P., Niz, G., Pérez-Ràfols, I., Ramírez-Pérez, C., Ravoux, C., Walther, M., Aguilar, J., Ahlen, S., Brooks, D., Claybaugh, T., Dawson, K., de la Macorra, A., Doel, P., Forero-Romero, J. E., Gaztañaga, E., Gontcho, S. Gontcho A, Honscheid, K., Kehoe, R., Kisner, T., Landriau, M., Levi, Michael E., Manera, M., Martini, P., Meisner, A., Miquel, R., Nie, J., Palanque-Delabrouille, N., Poppett, C., Rezaie, M., Rossi, G., Sanchez, E., Seo, H., Tarlé, G., Weaver, B. A., and Zhou, Z.
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract: Synthetic data sets are used in cosmology to test analysis procedures, to verify that systematic errors are well understood and to demonstrate that measurements are unbiased. In this work we describe the methods used to generate synthetic datasets of Lyman-$\alpha$ quasar spectra aimed for studies with the Dark Energy Spectroscopic Instrument (DESI). In particular, we focus on demonstrating that our simulations reproduces important features of real samples, making them suitable to test the analysis methods to be used in DESI and to place limits on systematic effects on measurements of Baryon Acoustic Oscillations (BAO). We present a set of mocks that reproduce the statistical properties of the DESI early data set with good agreement. Additionally, we use full survey synthetic data to forecast the BAO scale constraining power with DESI., Comment: 42 pages, 17 figures, 7 tables
Published: 2023

11. Reply to: Concerns regarding proposed groundwater Earth system boundary

Author: Bunn, S. E., Stewart-Koster, B., Ndehedehe, C., Gordon, C., Rockström, J., Gupta, J., Qin, D., and Lade, S. J.
Published: 2024
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12. How to spend one trillion dollars: the US decarbonization conundrum

Author: Christensen, Peter, Baylis, Patrick, v, Teevrat, Li, Shanjun, McCord, Gordon C., Muehlegger, Erich, Myers, Erica, Noble Smith, Emma, and Rapson, David S.
Published: 2024
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13. Optimal 1D Ly α forest power spectrum estimation – III. DESI early data

Author: Karaçaylı, Naim Göksel, Martini, Paul, Guy, Julien, Ravoux, Corentin, Karim, Marie Lynn Abdul, Armengaud, Eric, Walther, Michael, Aguilar, J, Ahlen, S, Bailey, S, Bautista, J, Beltran, SF, Brooks, D, Cabayol-Garcia, L, Chabanier, S, Chaussidon, E, Chaves-Montero, J, Dawson, K, de la Cruz, R, de la Macorra, A, Doel, P, Font-Ribera, A, Forero-Romero, JE, Gontcho, S Gontcho A, Gonzalez-Morales, AX, Gordon, C, Herrera-Alcantar, HK, Honscheid, K, Iršič, V, Ishak, M, Kehoe, R, Kisner, T, Kremin, A, Landriau, M, Le Guillou, L, Levi, ME, Lukić, Z, Meisner, A, Miquel, R, Moustakas, J, Mueller, E, Muñoz-Gutiérrez, A, Napolitano, L, Nie, J, Niz, G, Palanque-Delabrouille, N, Percival, WJ, Pieri, M, Poppett, C, Prada, F, Pérez-Ràfols, I, Ramírez-Pérez, C, Rossi, G, Sanchez, E, Seo, H, Sinigaglia, F, Tan, T, Tarlé, G, Wang, B, Weaver, BA, Yéche, C, and Zhou, Z
Subjects: Astronomical Sciences, Physical Sciences, methods: data analysis, intergalactic medium, quasars: absorption lines, Astronomical and Space Sciences, Astronomy & Astrophysics, Astronomical sciences, Particle and high energy physics, Space sciences
Abstract: The 1D power spectrum P1D of the Ly α forest provides important information about cosmological and astrophysical parameters, including constraints on warm dark matter models, the sum of the masses of the three neutrino species, and the thermal state of the intergalactic medium. We present the first measurement of P1D with the quadratic maximum likelihood estimator (QMLE) from the Dark Energy Spectroscopic Instrument (DESI) survey early data sample. This early sample of 54 600 quasars is already comparable in size to the largest previous studies, and we conduct a thorough investigation of numerous instrumental and analysis systematic errors to evaluate their impact on DESI data with QMLE. We demonstrate the excellent performance of the spectroscopic pipeline noise estimation and the impressive accuracy of the spectrograph resolution matrix with 2D image simulations of raw DESI images that we processed with the DESI spectroscopic pipeline. We also study metal line contamination and noise calibration systematics with quasar spectra on the red side of the Ly α emission line. In a companion paper, we present a similar analysis based on the Fast Fourier Transform estimate of the power spectrum. We conclude with a comparison of these two approaches and discuss the key sources of systematic error that we need to address with the upcoming DESI Year 1 analysis.
Published: 2024

14. The VALTIVE1 study protocol: a study for the validation of Tie2 as the first tumour vascular response biomarker for VEGF inhibitors

Author: Margherita Carucci, Andrew Clamp, Cong Zhou, Chris Hurt, Rosalind Glasspool, Phillip J. Monaghan, Sally Thirkettle, Michael Wheatley, Madia Mahmood, Monica Narasimham, Tracy Cox, Hilary Morrison, Susan Campbell, Annmarie Nelson, Daniella Holland-Hart, Noreen Hopewell-Kelly, Abin Thomas, Catharine Porter, Magdalena Slusarczyk, Alys Irving, Caroline Dive, Richard Adams, and Gordon C. Jayson
Subjects: Clinical trial, Ovarian cancer, VEGFi, Tie2, Clinical decision making, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract: Abstract Background Anti-angiogenic, VEGF inhibitors (VEGFi) increase progression-free survival (PFS) and, in some cases, overall survival in many solid tumours. However, their use has been compromised by a lack of informative biomarkers. We have shown that plasma Tie2 is the first tumour vascular response biomarker for VEGFi in ovarian, colorectal and gall bladder cancer: If plasma Tie2 concentrations do not change after 9 weeks of treatment with a VEGFi, the patient does not benefit, whereas a confirmed reduction of at least 10% plasma Tie2 defines a vascular response with a hazard ratio (HR) for PFS of 0.56. The aim of the VALTIVE1 study is to validate the utility of plasma Tie2 as a vascular response biomarker and to optimise the Tie2-definition of vascular response so that the subsequent randomised discontinuation VALTIVE2 study can be powered optimally. Methods VALTIVE1 is a multi-centre, single arm, non-interventional biomarker study, with a sample size of 205 participants (176 bevacizumab-treated participants + 29 participants receiving bevacizumab and olaparib/PARPi), who are 16 years or older, have FIGO stage IIIc/IV ovarian cancer on treatment with first-line platinum-based chemotherapy and bevacizumab. Their blood plasma samples will be collected before, during, and after treatment and the concentration of Tie2 will be determined. The primary objective is to define the PFS difference between Tie2-defined vascular responders and Tie2-defined vascular non-responders in patients receiving bevacizumab for high-risk Ovarian Cancer. Secondary objectives include defining the relationship between Tie2-defined vascular progression and disease progression assessed according to RECIST 1.1 criteria and assessing the impact of PARPi on the plasma concentration of Tie2 and, therefore, the decision-making utility of Tie2 as a vascular response biomarker for bevacizumab during combined bevacizumab-PARPi maintenance. Discussion There is an urgent need to establish a test that tells patients and their doctors when VEGFi are working and when they stop working. The data generated from this study will be used to design a second trial aiming to prove conclusively the value of the Tie2 test. Trial registration ClinicalTrials.gov identifier: NCT04523116. Registered on 21 Aug 2020.
Published: 2024
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15. Leveraging AI and patient metadata to develop a novel risk score for skin cancer detection

Author: Shafiqul Islam, Gordon C. Wishart, Joseph Walls, Per Hall, Alba G. Seco de Herrera, John Q. Gan, and Haider Raza
Subjects: Medicine, Science
Abstract: Abstract Melanoma of the skin is the 17th most common cancer worldwide. Early detection of suspicious skin lesions (melanoma) can increase 5-year survival rates by 20%. The 7-point checklist (7PCL) has been extensively used to suggest urgent referrals for patients with a possible melanoma. However, the 7PCL method only considers seven meta-features to calculate a risk score and is only relevant for patients with suspected melanoma. There are limited studies on the extensive use of patient metadata for the detection of all skin cancer subtypes. This study investigates artificial intelligence (AI) models that utilise patient metadata consisting of 23 attributes for suspicious skin lesion detection. We have identified a new set of most important risk factors, namely “C4C risk factors”, which is not just for melanoma, but for all types of skin cancer. The performance of the C4C risk factors for suspicious skin lesion detection is compared to that of the 7PCL and the Williams risk factors that predict the lifetime risk of melanoma. Our proposed AI framework ensembles five machine learning models and identifies seven new skin cancer risk factors: lesion pink, lesion size, lesion colour, lesion inflamed, lesion shape, lesion age, and natural hair colour, which achieved a sensitivity of $$80.46\pm 2.50\%$$ 80.46 ± 2.50 % and a specificity of $$62.09\pm 1.90\%$$ 62.09 ± 1.90 % in detecting suspicious skin lesions when evaluated using the metadata of 53,601 skin lesions collected from different skin cancer diagnostic clinics across the UK, significantly outperforming the 7PCL-based method (sensitivity $$68.09\pm 2.10\%$$ 68.09 ± 2.10 % , specificity $$61.07\pm 0.90\%$$ 61.07 ± 0.90 % ) and the Williams risk factors (sensitivity $$66.32\pm 1.90\%$$ 66.32 ± 1.90 % , specificity $$61.71\pm 0.6\%$$ 61.71 ± 0.6 % ). Furthermore, through weighting the seven new risk factors we came up with a new risk score, namely “C4C risk score”, which alone achieved a sensitivity of $$76.09\pm 1.20\%$$ 76.09 ± 1.20 % and a specificity of $$61.71\pm 0.50\%$$ 61.71 ± 0.50 % , significantly outperforming the 7PCL-based risk score (sensitivity $$73.91\pm 1.10\%$$ 73.91 ± 1.10 % , specificity $$49.49\pm 0.50\%$$ 49.49 ± 0.50 % ) and the Williams risk score (sensitivity $$60.68\pm 1.30\%$$ 60.68 ± 1.30 % , specificity $$60.87\pm 0.80\%$$ 60.87 ± 0.80 % ). Finally, fusing the C4C risk factors with the 7PCL and Williams risk factors achieved the best performance, with a sensitivity of $$85.24\pm 2.20\%$$ 85.24 ± 2.20 % and a specificity of $$61.12\pm 0.90\%$$ 61.12 ± 0.90 % . We believe that fusing these newly found risk factors and new risk score with image data will further boost the AI model performance for suspicious skin lesion detection. Hence, the new set of skin cancer risk factors has the potential to be used to modify current skin cancer referral guidelines for all skin cancer subtypes, including melanoma.
Published: 2024
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16. Variability, flaring and coherence -- the complementarity of the maser and superradiance regimes

Author: Houde, Martin, Rajabi, Fereshteh, MacLeod, Gordon C., Goedhart, Sharmila, Tanabe, Yoshihiro, Heever, Stefanus P. van den, Wyenberg, Christopher M., and Yonekura, Yoshinori
Subjects: Astrophysics - Astrophysics of Galaxies
Abstract: We discuss the role that coherence phenomena can have on the intensity variability of spectral lines associated with maser radiation. We do so by introducing the fundamental cooperative radiation phenomenon of (Dicke's) superradiance and discuss its complementary nature to the maser action, as well as its role in the flaring behaviour of some maser sources. We will consider examples of observational diagnostics that can help discriminate between the two, and identify superradiance as the source of the latter. More precisely, we show how superradiance readily accounts for the different time-scales observed in the multi-wavelength monitoring of the periodic flaring in G9.62+0.20E., Comment: 15 pages, 11 figures
Published: 2023

17. Optimal 1D Ly$\alpha$ Forest Power Spectrum Estimation -- III. DESI early data

Author: Karaçaylı, Naim Göksel, Martini, Paul, Guy, Julien, Ravoux, Corentin, Karim, Marie Lynn Abdul, Armengaud, Eric, Walther, Michael, Aguilar, J., Ahlen, S., Bailey, S., Bautista, J., Beltran, S. F., Brooks, D., Cabayol-Garcia, L., Chabanier, S., Chaussidon, E., Chaves-Montero, J., Dawson, K., de la Cruz, R., de la Macorra, A., Doel, P., Font-Ribera, A., Forero-Romero, J. E., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Gordon, C., Herrera-Alcantar, H. K, Honscheid, K., Iršič, V., Ishak, M., Kehoe, R., Kisner, T., Kremin, A., Landriau, M., Guillou, L. Le, Levi, M. E., Lukić, Z., Meisner, A., Miquel, R., Moustakas, J., Mueller, E., Muñoz-Gutiérrez, A., Napolitano, L., Nie, J., Niz, G., Palanque-Delabrouille, N., Percival, W. J., Pieri, M., Poppett, C., Prada, F., Pérez-Ràfols, I., Ramírez-Pérez, C., Rossi, G., Sanchez, E., Seo, H., Sinigaglia, F., Tan, T., Tarlé, G., Wang, B., Weaver, B. A., Yèche, C., and Zhou, Z.
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract: The one-dimensional power spectrum $P_{\mathrm{1D}}$ of the Ly$\alpha$ forest provides important information about cosmological and astrophysical parameters, including constraints on warm dark matter models, the sum of the masses of the three neutrino species, and the thermal state of the intergalactic medium. We present the first measurement of $P_{\mathrm{1D}}$ with the quadratic maximum likelihood estimator (QMLE) from the Dark Energy Spectroscopic Instrument (DESI) survey early data sample. This early sample of $54~600$ quasars is already comparable in size to the largest previous studies, and we conduct a thorough investigation of numerous instrumental and analysis systematic errors to evaluate their impact on DESI data with QMLE. We demonstrate the excellent performance of the spectroscopic pipeline noise estimation and the impressive accuracy of the spectrograph resolution matrix with two-dimensional image simulations of raw DESI images that we processed with the DESI spectroscopic pipeline. We also study metal line contamination and noise calibration systematics with quasar spectra on the red side of the Ly$\alpha$ emission line. In a companion paper, we present a similar analysis based on the Fast Fourier Transform estimate of the power spectrum. We conclude with a comparison of these two approaches and implications for the upcoming DESI Year 1 analysis., Comment: 23 pages, 20 figures. To be published in MNRAS
Published: 2023

18. The Lyman-$\alpha$ forest catalog from the Dark Energy Spectroscopic Instrument Early Data Release

Author: Ramírez-Pérez, César, Pérez-Ràfols, Ignasi, Font-Ribera, Andreu, Karim, M. Abdul, Armengaud, E., Bautista, J., Beltran, S. F., Cabayol-Garcia, L., Cai, Z., Chabanier, S., Chaussidon, E., Chaves-Montero, J., Cuceu, A., de la Cruz, R., García-Bellido, J., Gonzalez-Morales, A. X., Gordon, C., Herrera-Alcantar, H. K., Iršič, V., Ishak, M., Karaçaylı, N. G., Lukić, Zarija, Manser, C. J., Montero-Camacho, P., Napolitano, L., Niz, G., Pieri, M., Ravoux, C., Sinigaglia, F., Tan, T., Walther, M., Wang, B., Aguilar, J., Ahlen, S., Bailey, S., Brooks, D., Claybaugh, T., Dawson, K., de la Macorra, A., Dhungana, G., Doel, P., Fanning, K., Forero-Romero, J. E., Gontcho, S. Gontcho A, Guy, J., Honscheid, K., Kehoe, R., Kisner, T., Landriau, M., Guillou, L. Le, Levi, M. E., Magneville, C., Martini, P., Meisner, A., Miquel, R., Moustakas, J., Mueller, E., Muñoz-Gutiérrez, A., Nie, J., Palanque-Delabrouille, N., Percival, W. J., Rossi, G., Sanchez, E., Schlafly, E. F., Schlegel, D., Seo, H., Tarlé, G., Weaver, B. A., Yèche, C., and Zhou, Z.
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract: We present and validate the catalog of Lyman-$\alpha$ forest fluctuations for 3D analyses using the Early Data Release (EDR) from the Dark Energy Spectroscopic Instrument (DESI) survey. We used 88,511 quasars collected from DESI Survey Validation (SV) data and the first two months of the main survey (M2). We present several improvements to the method used to extract the Lyman-$\alpha$ absorption fluctuations performed in previous analyses from the Sloan Digital Sky Survey (SDSS). In particular, we modify the weighting scheme and show that it can improve the precision of the correlation function measurement by more than 20%. This catalog can be downloaded from https://data.desi.lbl.gov/public/edr/vac/edr/lya/fuji/v0.3 and it will be used in the near future for the first DESI measurements of the 3D correlations in the Lyman-$\alpha$ forest.
Published: 2023

19. The Early Data Release of the Dark Energy Spectroscopic Instrument

Author: DESI Collaboration, Adame, A. G., Aguilar, J., Ahlen, S., Alam, S., Aldering, G., Alexander, D. M., Alfarsy, R., Prieto, C. Allende, Alvarez, M., Alves, O., Anand, A., Andrade-Oliveira, F., Armengaud, E., Asorey, J., Avila, S., Aviles, A., Bailey, S., Balaguera-Antolínez, A., Ballester, O., Baltay, C., Bault, A., Bautista, J., Behera, J., Beltran, S. F., BenZvi, S., Silva, L. Beraldo e, Bermejo-Climent, J. R., Berti, A., Besuner, R., Beutler, F., Bianchi, D., Blake, C., Blum, R., Bolton, A. S., Brieden, S., Brodzeller, A., Brooks, D., Brown, Z., Buckley-Geer, E., Burtin, E., Cabayol-Garcia, L., Cai, Z., Canning, R., Cardiel-Sas, L., Rosell, A. Carnero, Castander, F. J., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chaves-Montero, J., Chen, S., Chen, X., Chuang, C., Claybaugh, T., Cole, S., Cooper, A. P., Cuceu, A., Davis, T. M., Dawson, K., de Belsunce, R., de la Cruz, R., de la Macorra, A., Della Costa, J., de Mattia, A., Demina, R., Demirbozan, U., DeRose, J., Dey, A., Dey, B., Dhungana, G., Ding, J., Ding, Z., Doel, P., Doshi, R., Douglass, K., Edge, A., Eftekharzadeh, S., Eisenstein, D. J., Elliott, A., Escoffier, S., Fagrelius, P., Fan, X., Fanning, K., Fawcett, V. A., Ferraro, S., Ereza, J., Flaugher, B., Font-Ribera, A., Forero-Sánchez, D., Forero-Romero, J. E., Frenk, C. S., Gänsicke, B. T., García, L. Á., García-Bellido, J., Garcia-Quintero, C., Garrison, L. H., Gil-Marín, H., Golden-Marx, J., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Gonzalez-Perez, V., Gordon, C., Graur, O., Green, D., Gruen, D., Guy, J., Hadzhiyska, B., Hahn, C., Han, J. J., Hanif, M. M. S, Herrera-Alcantar, H. K., Honscheid, K., Hou, J., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Jacques, A., Jana, A., Jiang, L., Jimenez, J., Jing, Y. P., Joudaki, S., Jullo, E., Juneau, S., Kizhuprakkat, N., Karaçaylı, N. G., Karim, T., Kehoe, R., Kent, S., Khederlarian, A., Kim, S., Kirkby, D., Kisner, T., Kitaura, F., Kneib, J., Koposov, S. E., Kovács, A., Kremin, A., Krolewski, A., L'Huillier, B., Lahav, O., Lambert, A., Lamman, C., Lan, T. -W., Landriau, M., Lang, D., Lange, J. U., Lasker, J., Leauthaud, A., Guillou, L. Le, Levi, M. E., Li, T. S., Linder, E., Lyons, A., Magneville, C., Manera, M., Manser, C. J., Margala, D., Martini, P., McDonald, P., Medina, G. E., Medina-Varela, L., Meisner, A., Mena-Fernández, J., Meneses-Rizo, J., Mezcua, M., Miquel, R., Montero-Camacho, P., Moon, J., Moore, S., Moustakas, J., Mueller, E., Mundet, J., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Napolitano, L., Neveux, R., Newman, J. A., Nie, J., Nikutta, R., Niz, G., Norberg, P., Noriega, H. E., Paillas, E., Palanque-Delabrouille, N., Palmese, A., Zhiwei, P., Parkinson, D., Penmetsa, S., Percival, W. J., Pérez-Fernández, A., Pérez-Ràfols, I., Pieri, M., Poppett, C., Porredon, A., Pothier, S., Prada, F., Pucha, R., Raichoor, A., Ramírez-Pérez, C., Ramirez-Solano, S., Rashkovetskyi, M., Ravoux, C., Rocher, A., Rockosi, C., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Sabiu, C. G., Said, K., Saintonge, A., Samushia, L., Sanchez, E., Saulder, C., Schaan, E., Schlafly, E. F., Schlegel, D., Scholte, D., Schubnell, M., Seo, H., Shafieloo, A., Sharples, R., Sheu, W., Silber, J., Sinigaglia, F., Siudek, M., Slepian, Z., Smith, A., Soumagnac, M. T., Sprayberry, D., Stephey, L., Suárez-Pérez, J., Sun, Z., Tan, T., Tarlé, G., Tojeiro, R., Ureña-López, L. A., Vaisakh, R., Valcin, D., Valdes, F., Valluri, M., Vargas-Magaña, M., Variu, A., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, N., Wechsler, R. H., White, M., Xie, Y., Yang, J., Yèche, C., Yu, J., Yuan, S., Zhang, H., Zhang, Z., Zhao, C., Zheng, Z., Zhou, R., Zhou, Z., Zou, H., Zou, S., and Zu, Y.
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract: The Dark Energy Spectroscopic Instrument (DESI) completed its five-month Survey Validation in May 2021. Spectra of stellar and extragalactic targets from Survey Validation constitute the first major data sample from the DESI survey. This paper describes the public release of those spectra, the catalogs of derived properties, and the intermediate data products. In total, the public release includes good-quality spectral information from 466,447 objects targeted as part of the Milky Way Survey, 428,758 as part of the Bright Galaxy Survey, 227,318 as part of the Luminous Red Galaxy sample, 437,664 as part of the Emission Line Galaxy sample, and 76,079 as part of the Quasar sample. In addition, the release includes spectral information from 137,148 objects that expand the scope beyond the primary samples as part of a series of secondary programs. Here, we describe the spectral data, data quality, data products, Large-Scale Structure science catalogs, access to the data, and references that provide relevant background to using these spectra., Comment: 43 pages, 7 figures, 17 tables, accepted for publication in the Astronomical Journal
Published: 2023
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20. Validation of the Scientific Program for the Dark Energy Spectroscopic Instrument

Author: DESI Collaboration, Adame, A. G., Aguilar, J., Ahlen, S., Alam, S., Aldering, G., Alexander, D. M., Alfarsy, R., Prieto, C. Allende, Alvarez, M., Alves, O., Anand, A., Andrade-Oliveira, F., Armengaud, E., Asorey, J., Avila, S., Aviles, A., Bailey, S., Balaguera-Antolínez, A., Ballester, O., Baltay, C., Bault, A., Bautista, J., Behera, J., Beltran, S. F., BenZvi, S., Silva, L. Beraldo e, Bermejo-Climent, J. R., Berti, A., Besuner, R., Beutler, F., Bianchi, D., Blake, C., Blum, R., Bolton, A. S., Brieden, S., Brodzeller, A., Brooks, D., Brown, Z., Buckley-Geer, E., Burtin, E., Cabayol-Garcia, L., Cai, Z., Canning, R., Cardiel-Sas, L., Rosell, A. Carnero, Castander, F. J., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chaves-Montero, J., Chen, S., Chuang, C., Claybaugh, T., Cole, S., Cooper, A. P., Cuceu, A., Davis, T. M., Dawson, K., de Belsunce, R., de la Cruz, R., de la Macorra, A., de Mattia, A., Demina, R., Demirbozan, U., DeRose, J., Dey, A., Dey, B., Dhungana, G., Ding, J., Ding, Z., Doel, P., Doshi, R., Douglass, K., Edge, A., Eftekharzadeh, S., Eisenstein, D. J., Elliott, A., Escoffier, S., Fagrelius, P., Fan, X., Fanning, K., Fawcett, V. A., Ferraro, S., Ereza, J., Flaugher, B., Font-Ribera, A., Forero-Sánchez, D., Forero-Romero, J. E., Frenk, C. S., Gänsicke, B. T., García, L. Á., García-Bellido, J., Garcia-Quintero, C., Garrison, L. H., Gil-Marín, H., Golden-Marx, J., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Gonzalez-Perez, V., Gordon, C., Graur, O., Green, D., Gruen, D., Guy, J., Hadzhiyska, B., Hahn, C., Han, J. J., Hanif, M. M. S, Herrera-Alcantar, H. K., Honscheid, K., Hou, J., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Jana, A., Jiang, L., Jimenez, J., Jing, Y. P., Joudaki, S., Joyce, R., Jullo, E., Juneau, S., Kizhuprakkat, N., Karaçaylı, N. G., Karim, T., Kehoe, R., Kent, S., Khederlarian, A., Kim, S., Kirkby, D., Kisner, T., Kitaura, F., Kneib, J., Koposov, S. E., Kovács, A., Kremin, A., Krolewski, A., L'Huillier, B., Lahav, O., Lambert, A., Lamman, C., Lan, T. -W., Landriau, M., Lang, D., Lange, J. U., Lasker, J., Guillou, L. Le, Leauthaud, A., Levi, M. E., Li, T. S., Linder, E., Lyons, A., Magneville, C., Manera, M., Manser, C. J., Margala, D., Martini, P., McDonald, P., Medina, G. E., Medina-Varela, L., Meisner, A., Mena-Fernández, J., Meneses-Rizo, J., Mezcua, M., Miquel, R., Montero-Camacho, P., Moon, J., Moore, S., Moustakas, J., Mueller, E., Mundet, J., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Napolitano, L., Neveux, R., Newman, J. A., Nie, J., Niz, G., Norberg, P., Noriega, H. E., Paillas, E., Palanque-Delabrouille, N., Palmese, A., Zhiwei, P., Parkinson, D., Penmetsa, S., Percival, W. J., Pérez-Fernández, A., Pérez-Ràfols, I., Pieri, M., Poppett, C., Porredon, A., Prada, F., Pucha, R., Raichoor, A., Ramírez-Pérez, C., Ramirez-Solano, S., Rashkovetskyi, M., Ravoux, C., Rocher, A., Rockosi, C., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Sabiu, C. G., Said, K., Saintonge, A., Samushia, L., Sanchez, E., Saulder, C., Schaan, E., Schlafly, E. F., Schlegel, D., Scholte, D., Schubnell, M., Seo, H., Shafieloo, A., Sharples, R., Sheu, W., Silber, J., Sinigaglia, F., Siudek, M., Slepian, Z., Smith, A., Sprayberry, D., Stephey, L., Suárez-Pérez, J., Sun, Z., Tan, T., Tarlé, G., Tojeiro, R., Ureña-López, L. A., Vaisakh, R., Valcin, D., Valdes, F., Valluri, M., Vargas-Magaña, M., Variu, A., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, N., Wechsler, R. H., White, M., Xie, Y., Yang, J., Yèche, C., Yu, J., Yuan, S., Zhang, H., Zhang, Z., Zhao, C., Zheng, Z., Zhou, R., Zhou, Z., Zou, H., Zou, S., and Zu, Y.
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract: The Dark Energy Spectroscopic Instrument (DESI) was designed to conduct a survey covering 14,000 deg$^2$ over five years to constrain the cosmic expansion history through precise measurements of Baryon Acoustic Oscillations (BAO). The scientific program for DESI was evaluated during a five month Survey Validation (SV) campaign before beginning full operations. This program produced deep spectra of tens of thousands of objects from each of the stellar (MWS), bright galaxy (BGS), luminous red galaxy (LRG), emission line galaxy (ELG), and quasar target classes. These SV spectra were used to optimize redshift distributions, characterize exposure times, determine calibration procedures, and assess observational overheads for the five-year program. In this paper, we present the final target selection algorithms, redshift distributions, and projected cosmology constraints resulting from those studies. We also present a `One-Percent survey' conducted at the conclusion of Survey Validation covering 140 deg$^2$ using the final target selection algorithms with exposures of a depth typical of the main survey. The Survey Validation indicates that DESI will be able to complete the full 14,000 deg$^2$ program with spectroscopically-confirmed targets from the MWS, BGS, LRG, ELG, and quasar programs with total sample sizes of 7.2, 13.8, 7.46, 15.7, and 2.87 million, respectively. These samples will allow exploration of the Milky Way halo, clustering on all scales, and BAO measurements with a statistical precision of 0.28% over the redshift interval $z<1.1$, 0.39% over the redshift interval $1.1
Published: 2023
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21. The VALTIVE1 study protocol: a study for the validation of Tie2 as the first tumour vascular response biomarker for VEGF inhibitors

Author: Carucci, Margherita, Clamp, Andrew, Zhou, Cong, Hurt, Chris, Glasspool, Rosalind, Monaghan, Phillip J., Thirkettle, Sally, Wheatley, Michael, Mahmood, Madia, Narasimham, Monica, Cox, Tracy, Morrison, Hilary, Campbell, Susan, Nelson, Annmarie, Holland-Hart, Daniella, Hopewell-Kelly, Noreen, Thomas, Abin, Porter, Catharine, Slusarczyk, Magdalena, Irving, Alys, Dive, Caroline, Adams, Richard, and Jayson, Gordon C.
Published: 2024
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22. Leveraging AI and patient metadata to develop a novel risk score for skin cancer detection

Author: Islam, Shafiqul, Wishart, Gordon C., Walls, Joseph, Hall, Per, Seco de Herrera, Alba G., Gan, John Q., and Raza, Haider
Published: 2024
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23. Benzoxazole-derivatives enhance progranulin expression and reverse the aberrant lysosomal proteome caused by GRN haploinsufficiency

Author: Tesla, Rachel, Guhl, Charlotte, Werthmann, Gordon C., Dixon, Danielle, Cenik, Basar, Addepalli, Yesu, Liang, Jue, Fass, Daniel M., Rosenthal, Zachary, Haggarty, Stephen J., Williams, Noelle S., Posner, Bruce A., Ready, Joseph M., and Herz, Joachim
Published: 2024
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24. Epigenetic modulation through BET bromodomain inhibitors as a novel therapeutic strategy for progranulin-deficient frontotemporal dementia

Author: Rosenthal, Zachary C., Fass, Daniel M., Payne, N. Connor, She, Angela, Patnaik, Debasis, Hennig, Krista M., Tesla, Rachel, Werthmann, Gordon C., Guhl, Charlotte, Reis, Surya A., Wang, Xiaoyu, Chen, Yueting, Placzek, Michael, Williams, Noelle S., Hooker, Jacob, Herz, Joachim, Mazitschek, Ralph, and Haggarty, Stephen J.
Published: 2024
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25. Pandemic lockdowns: who feels coerced and why? - a study on perceived coercion, perceived pressures and procedural justice during the UK COVID-19 lockdowns

Author: Ranieri, V., Gordon, C., Kamboj, S. K., and Edwards, S. J.
Published: 2024
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26. An updated PREDICT breast cancer prognostic model including the benefits and harms of radiotherapy

Author: Grootes, Isabelle, Wishart, Gordon C., and Pharoah, Paul David Peter
Published: 2024
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27. Benzoxazole-derivatives enhance progranulin expression and reverse the aberrant lysosomal proteome caused by GRN haploinsufficiency

Author: Rachel Tesla, Charlotte Guhl, Gordon C. Werthmann, Danielle Dixon, Basar Cenik, Yesu Addepalli, Jue Liang, Daniel M. Fass, Zachary Rosenthal, Stephen J. Haggarty, Noelle S. Williams, Bruce A. Posner, Joseph M. Ready, and Joachim Herz
Subjects: Science
Abstract: Abstract Heterozygous loss-of-function mutations in the GRN gene are a major cause of hereditary frontotemporal dementia. The mechanisms linking frontotemporal dementia pathogenesis to progranulin deficiency are not well understood, and there is currently no treatment. Our strategy to prevent the onset and progression of frontotemporal dementia in patients with GRN mutations is to utilize small molecule positive regulators of GRN expression to boost progranulin levels from the remaining functional GRN allele, thus restoring progranulin levels back to normal within the brain. This work describes a series of blood-brain-barrier-penetrant small molecules which significantly increase progranulin protein levels in human cellular models, correct progranulin protein deficiency in Grn +/− mouse brains, and reverse lysosomal proteome aberrations, a phenotypic hallmark of frontotemporal dementia, more efficiently than the previously described small molecule suberoylanilide hydroxamic acid. These molecules will allow further elucidation of the cellular functions of progranulin and its role in frontotemporal dementia and will also serve as lead structures for further drug development.
Published: 2024
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28. APPENDIX

Author: RAUSSER, GORDON C., primary and DEAN, GERALD W., additional
Published: 2024
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29. Uncertainty and Decision-Making in Water Resources.

Author: Rausser, Gordon C., primary and Dean, Gerald W., additional
Published: 2024
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30. Tracing Water Masers at their Smallest Scale with VLBI

Author: Vorster, Jakobus M., Chibueze, James O., Hirota, Tomoya, and MacLeod, Gordon C.
Subjects: Astrophysics - Solar and Stellar Astrophysics
Abstract: The high-mass star-forming region NGC6334I-MM1 underwent an energetic accretion event in January 2015. We report the large-scale ($10 - 100$ AU) and small-scale ($\sim 1$ AU) changes in spatial and velocity structures of 22 GHz water masers as observed with VERA before and during the accretion burst. The masers in the northern bow-shock CM2-W2 brightened, and better traced a bow structure during the burst. In the southern regions, there was both activation and disappearance of associations before and during the burst. We measured the amplitudes, central velocities and FWHMs of about 20 features in each epoch. We found that the linear scale of the brightest feature in CM2-W2 grew from 0.6 AU before the burst to 1.4 AU after the burst, possibly indicating that a larger volume of gas was able to sustain masing action as a consequence of the accretion burst. This feature also had a rapid (0.2 yr) brightness increase by a factor of four, which has been previously reported in long-term single-dish monitoring. We propose that the water maser flare could be explained by an increase of the collisional pump rate due to radiative heating of H$_2$ by increased high energy radiation (UV or X-ray) from the inner protostellar core. We also describe the spot and spectral method of maser proper motion calculations. We argue that for high spectral resolution observations the spectral method is more robust for calculating proper motions than the spot method., Comment: 6 pages, 2 figures, to be published in the South African Institute for Physics 2022 conference proceedings
Published: 2022

31. Editorial: Advances in biomonitoring of African aquatic ecosystems, volume II

Author: Francis O. Arimoro, Frank O. Masese, and Gordon C. O'Brien
Subjects: biomonitoring, riverine ecosystems, sustainability, Africa, water resource management, conservation, Environmental technology. Sanitary engineering, TD1-1066
Published: 2024
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32. Acute effect of resistive aquatic high-intensity interval training on metabolic costs in adults

Author: Manny M. Y. Kwok, Shamay S. M. Ng, Y. M. Ng, Gordon C. C. Tan, P. P. Huang, Y. Zhang, and Billy C. L. So
Subjects: aquatic exercise, high interval, resistive exercise, physical activity, metabolism, Sports, GV557-1198.995
Abstract: BackgroundThe effects of Aquatic High-Intensity Interval Training (AHIIT) and resistive AHIIT (Resistive AHIIT) to improve metabolic responses were not yet known.ObjectiveThis study was to compare the metabolic responses and perceived effort in young healthy adults in a single session of AHIIT and resistive AHIIT.Methods20 healthy subjects (9 females, 11 males) performed a stationary running at a matched exercise intensity prior AHIIT and resistive AHIIT [10 × 1-min bouts of stationary running at 90% maximum heart rate (HR max) separated by 1-min active recovery] to examine the metabolic and cardiometabolic outcomes. Mixed effects models were applied to analyze the effects of group, time, and the interaction between group and time on both outcomes. The level of correlations between metabolic variables was checked by Pearson's linear correlation.ResultsThere are significant differences on pre and post resting energy expenditure (REE) within both AHIIT and resistive AHIIT groups (p
Published: 2024
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33. Enhancement of Subcutaneous Islet Transplant Performance by Collagen 1 Gel

Author: Anna French, Jennifer Hollister-Lock, Brooke A. Sullivan, Eline Stas, Albert J. Hwa, Gordon C. Weir, and Susan Bonner-Weir
Subjects: Medicine
Abstract: Human islets can be transplanted into the portal vein for T1 diabetes, and a similar procedure is being used in a clinical trial for stem cell–derived beta-like cells. Efforts have been underway to find an alternative transplant site that will foster better islet cell survival and function. Although conceptually attractive, the subcutaneous (SC) site has yielded disappointing results, in spite of some improvements resulting from more attention paid to vascularization and differentiation factors, including collagen. We developed a method to transplant rat islets in a disk of type 1 collagen gel and found improved efficacy of these transplants. Survival of islets following transplantation (tx) was determined by comparing insulin content of the graft to that of the pre-transplant islets from the same isolation. At 14 days after transplantation, grafts of the disks had more than double the recovered insulin than islets transplanted in ungelled collagen. SC grafts of disks had similar insulin content to grafts in a kidney site and in epididymal fat pads. In vivo disks underwent contraction to 10% of initial volume within 24 h but the islets remained healthy and well distributed. Whole mount imaging showed that residual donor vascular cells within the islets expanded and connected to ingrowing host blood vessels. Islets (400 rat islet equivalents (IEQ)) in the collagen disks transplanted into an SC site of NOD scid IL2R gammanull (NSG) mice reversed streptozotocin (STZ)-induced diabetes within 10 days as effectively as transplants in the kidney site. Thus, a simple change of placing islets into a gel of collagen 1 prior to transplantation allowed a prompt reversal of STZ-induced diabetes using SC site.
Published: 2024
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34. Gut microbiota alteration - Cancer relationships and synbiotic roles in cancer therapies

Author: Adekunle Rowaiye, Gordon C. Ibeanu, Doofan Bur, Sandra Nnadi, Odinaka E. Mgbeke, and Ugonna Morikwe
Subjects: Cancer, synbiotics, therapies, microbiota, prebiotic, probiotic, Microbiology, QR1-502
Abstract: Cancer poses a significant global health challenge, with 10 million deaths and 19.3 million new cases reported annually. This review aims to investigate the emerging field of synbiotics and their potential to enhance the effectiveness of cancer therapies. By conducting a thorough analysis of preclinical and clinical studies, this review clarifies the various mechanisms through which synbiotics improve the efficacy of conventional cancer treatments, such as chemotherapy, immunotherapy, surgery, and radiotherapy. A search of literature on the anti-cancer efficacy of synbiotics was performed using the PubMed database and Google Scholar search engine to find important original research and review publications. A selection, analysis, and discussion of related English-language papers were conducted. This review unravels the intricate connections between microbiota and cancer therapeutics, harnessing the power of synbiotics as a promising strategy to improve treatment outcomes and elevate the standard of care in oncology. Further research is required to establish the efficacy and long-term safety of synbiotics, the ideal prebiotic-probiotic combinations, and the distinct microbiota signatures of different cancer types for the development of future synbiotics.
Published: 2024
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35. The DESI Survey Validation: Results from Visual Inspection of the Quasar Survey Spectra

Author: Alexander, David M, Davis, Tamara M, Chaussidon, E, Fawcett, VA, Gonzalez-Morales, Alma X, Lan, Ting-Wen, Yèche, Christophe, Ahlen, S, Aguilar, JN, Armengaud, E, Bailey, S, Brooks, D, Cai, Z, Canning, R, Carr, A, Chabanier, S, Cousinou, Marie-Claude, Dawson, K, de la Macorra, A, Dey, A, Dey, Biprateep, Dhungana, G, Edge, AC, Eftekharzadeh, S, Fanning, K, Farr, James, Font-Ribera, A, Garcia-Bellido, J, Garrison, Lehman, Gaztañaga, E, Gontcho, Satya Gontcho A, Gordon, C, Gonzalez, Stefany Guadalupe Medellin, Guy, J, Herrera-Alcantar, Hiram K, Jiang, L, Juneau, S, Karaçaylı, NG, Kehoe, R, Kisner, T, Kovács, A, Landriau, M, Levi, Michael E, Magneville, C, Martini, P, Meisner, Aaron M, Mezcua, M, Miquel, R, Camacho, P Montero, Moustakas, J, Muñoz-Gutiérrez, Andrea, Myers, Adam D, Nadathur, S, Napolitano, L, Nie, JD, Palanque-Delabrouille, N, Pan, Z, Percival, WJ, Pérez-Ràfols, I, Poppett, C, Prada, F, Ramírez-Pérez, César, Ravoux, C, Rosario, DJ, Schubnell, M, Tarlé, Gregory, Walther, M, Weiner, B, Youles, S, Zhou, Zhimin, Zou, H, and Zou, Siwei
Subjects: Space Sciences, Physical Sciences, Astronomical and Space Sciences, Astronomy & Astrophysics, Astronomical sciences, Particle and high energy physics
Abstract: A key component of the Dark Energy Spectroscopic Instrument (DESI) survey validation (SV) is a detailed visual inspection (VI) of the optical spectroscopic data to quantify key survey metrics. In this paper we present results from VI of the quasar survey using deep coadded SV spectra. We show that the majority (≈70%) of the main-survey targets are spectroscopically confirmed as quasars, with ≈16% galaxies, ≈6% stars, and ≈8% low-quality spectra lacking reliable features. A nonnegligible fraction of the quasars are misidentified by the standard spectroscopic pipeline, but we show that the majority can be recovered using post-pipeline “afterburner” quasar-identification approaches. We combine these “afterburners” with our standard pipeline to create a modified pipeline to increase the overall quasar yield. At the depth of the main DESI survey, both pipelines achieve a good-redshift purity (reliable redshifts measured within 3000 km s−1) of ≈99%; however, the modified pipeline recovers ≈94% of the visually inspected quasars, as compared to ≈86% from the standard pipeline. We demonstrate that both pipelines achieve a median redshift precision and accuracy of ≈100 km s−1 and ≈70 km s−1, respectively. We constructed composite spectra to investigate why some quasars are missed by the standard pipeline and find that they are more host-galaxy dominated (i.e., distant analogs of “Seyfert galaxies”) and/or more dust reddened than the standard-pipeline quasars. We also show example spectra to demonstrate the overall diversity of the DESI quasar sample and provide strong-lensing candidates where two targets contribute to a single spectrum.
Published: 2023

36. Radiometric sensitivity and resolution of synthetic tracking imaging for orbital debris monitoring

Author: Bahcivan, Hasan, Brady, David J., and Hageman, Gordon C.
Subjects: Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics, Physics - Optics
Abstract: We consider sampling and detection strategies for solar illuminated space debris. We argue that the lowest detectable debris cross section may be reduced by 10-100x by analysis of phase-space-pixels rather than single frame data. The phase-space-pixel is a weighted stacking of pixels corresponding to a test debris trajectory within the very wide camera field-of-view (FOV). To isolate debris signals from background, exposure time is set to match the time it takes a debris to transit through the instantaneous field of view. Debris signatures are detected though a generalized Hough transform of the data cube. Radiometric analysis of line integrals shows that that sub-cm objects in Low Earth Orbit can be detected and assigned full orbital parameters by this approach
Published: 2022

37. Placental Streptococcus agalactiae DNA is associated with neonatal unit admission and foetal pro-inflammatory cytokines in term infants

Author: Gaccioli, Francesca, Stephens, Katie, Sovio, Ulla, Jessop, Flora, Wong, Hilary S., Lager, Susanne, Cook, Emma, de Goffau, Marcus C., Le Doare, Kirsty, Peacock, Sharon J., Parkhill, Julian, Charnock-Jones, D. Stephen, and Smith, Gordon C. S.
Published: 2023
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38. Pharmacokinetics and Tolerability of Zibotentan in Patients with Concurrent Moderate Renal and Moderate Hepatic Impairment

Author: Mercier, Anne-Kristina, Sunnåker, Mikael, Ueckert, Sebastian, Pawlik, Tadeusz, Henricson, Emilia, Molodetskyi, Oleksandr, Law, Gordon C., Parker, Victoria E. R., and Oscarsson, Jan
Published: 2023
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39. Epigenetic modulation through BET bromodomain inhibitors as a novel therapeutic strategy for progranulin-deficient frontotemporal dementia

Author: Zachary C. Rosenthal, Daniel M. Fass, N. Connor Payne, Angela She, Debasis Patnaik, Krista M. Hennig, Rachel Tesla, Gordon C. Werthmann, Charlotte Guhl, Surya A. Reis, Xiaoyu Wang, Yueting Chen, Michael Placzek, Noelle S. Williams, Jacob Hooker, Joachim Herz, Ralph Mazitschek, and Stephen J. Haggarty
Subjects: Medicine, Science
Abstract: Abstract Frontotemporal dementia (FTD) is a debilitating neurodegenerative disorder with currently no disease-modifying treatment options available. Mutations in GRN are one of the most common genetic causes of FTD, near ubiquitously resulting in progranulin (PGRN) haploinsufficiency. Small molecules that can restore PGRN protein to healthy levels in individuals bearing a heterozygous GRN mutation may thus have therapeutic value. Here, we show that epigenetic modulation through bromodomain and extra-terminal domain (BET) inhibitors (BETi) potently enhance PGRN protein levels, both intracellularly and secreted forms, in human central nervous system (CNS)-relevant cell types, including in microglia-like cells. In terms of potential for disease modification, we show BETi treatment effectively restores PGRN levels in neural cells with a GRN mutation known to cause PGRN haploinsufficiency and FTD. We demonstrate that BETi can rapidly and durably enhance PGRN in neural progenitor cells (NPCs) in a manner dependent upon BET protein expression, suggesting a gain-of-function mechanism. We further describe a CNS-optimized BETi chemotype that potently engages endogenous BRD4 and enhances PGRN expression in neuronal cells. Our results reveal a new epigenetic target for treating PGRN-deficient forms of FTD and provide mechanistic insight to aid in translating this discovery into therapeutics.
Published: 2024
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40. The DESI Survey Validation: Results from Visual Inspection of the Quasar Survey Spectra

Author: Alexander, David M., Davis, Tamara M., Chaussidon, E., Fawcett, V. A., Gonzalez-Morales, Alma X., Lan, Ting-Wen, Yeche, Christophe, Ahlen, S., Aguilar, J. N., Armengaud, E., Bailey, S., Brooks, D., Cai, Z., Canning, R., Carr, A., Chabanier, S., Cousinou, Marie-Claude, Dawson, K., de la Macorra, A., Dey, A., Dey, Biprateep, Dhungana, G., Edge, A. C., Eftekharzadeh, S., Fanning, K., Farr, James, Font-Ribera, A., Garcia-Bellido, J., Garrison, Lehman, Gaztanaga, E., Gontcho, Satya Gontcho A, Gordon, C., Gonzalez, Stefany Guadalupe Medellin, Guy, J., Herrera-Alcantar, Hiram K., Jiang, L., Juneau, S., Karacayli, Naim, Kehoe, R., Kisner, T., Kovacs, A., Landriau, M., Levi, Michael E., Magneville, C., Martini, P., Meisner, Aaron M., Mezcua, M., Miquel, R., Camacho, P. Montero, Moustakas, J., Munoz-Gutierrez, Andrea, Myers, Adam D., Nadathur, S., Napolitano, L., Nie, J. D., Palanque-Delabrouille, N., Pan, Z., Percival, W. J., Perez-Rafols, I., Poppett, C., Prada, F., Ramirez-Perez, Cesar, Ravoux, C., Rosario, D. J., Schubnell, M., Tarle, Gregory, Walther, M., Weiner, B., Youles, S., Zhou, Zhimin, Zou, H., and Zou, Siwei
Subjects: Astrophysics - Astrophysics of Galaxies, Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract: A key component of the Dark Energy Spectroscopic Instrument (DESI) survey validation (SV) is a detailed visual inspection (VI) of the optical spectroscopic data to quantify key survey metrics. In this paper we present results from VI of the quasar survey using deep coadded SV spectra. We show that the majority (~70%) of the main-survey targets are spectroscopically confirmed as quasars, with ~16% galaxies, ~6% stars, and ~8% low-quality spectra lacking reliable features. A non-negligible fraction of the quasars are misidentified by the standard spectroscopic pipeline but we show that the majority can be recovered using post-pipeline "afterburner" quasar-identification approaches. We combine these "afterburners" with our standard pipeline to create a modified pipeline to improve the overall quasar yield. At the depth of the main DESI survey both pipelines achieve a good-redshift purity (reliable redshifts measured within 3000 km/s) of ~99%; however, the modified pipeline recovers ~94% of the visually inspected quasars, as compared to ~86% from the standard pipeline. We demonstrate that both pipelines achieve an median redshift precision and accuracy of ~100 km/s and ~70 km/s, respectively. We constructed composite spectra to investigate why some quasars are missed by the standard spectroscopic pipeline and find that they are more host-galaxy dominated (i.e., distant analogs of "Seyfert galaxies") and/or dust reddened than the standard-pipeline quasars. We also show example spectra to demonstrate the overall diversity of the DESI quasar sample and provide strong-lensing candidates where two targets contribute to a single spectrum., Comment: Astronomical journal (in press). 26 pages, 15 figures, 9 tables, one of a suite of 8 papers detailing targeting for DESI. Figure data available from Zenodo (see paper for details)
Published: 2022
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41. Long-term pathways analysis to assess the feasibility of sustainable land-use and food systems in Mexico

Author: González-Abraham, Charlotte, Flores-Santana, Cynthia, Rodríguez-Ramírez, Sonia, Olguín-Álvarez, Marcela, Flores-Martínez, Arturo, Torres Rojo, Juan Manuel, Bocco Verdinelli, Gerardo, Fernández Calleros, Claudia A, and McCord, Gordon C
Subjects: Nutrition, Life on Land, Climate Action, Zero Hunger, Environmental Sciences
Abstract: Mexico aims to develop highly productive and sustainable food systems that ensure national self-sufficiency. This paper employs an integrated land-use modeling tool—the FABLE Calculator—to estimate the degree of policy ambition required for the country to meet mid-century climate, conservation and production goals in the land-use sector. We generate national-level land-use pathways to mid-century in terms of agricultural production, land use change dynamics, greenhouse gas (GHG) emissions, and availability of land supporting biodiversity under varying assumptions of national policy and productivity changes. We estimate the effects of plausible efforts to achieve sustainability in land-use and food systems to 2050 against a business-as-usual benchmark. In the sustainable pathway, assumptions on agricultural land expansion, reforestation, and protected area expansion reflect existing and aspirational Mexican government policies aiming to improve crop yields, livestock productivity with silvopastoral systems, and GHG mitigation goals. We also model diets that evolve toward Mexican dietary guidelines for a healthier consumption of fats and oils as well as a substantial increase in the intake of fruits and vegetables, pulses, nuts, and fish. Results suggest that Mexico can feasibly adopt a sustainable land-use pathway that provides adequate nutrition for the population by 2050, limit agricultural expansion, reduce GHG emissions, and expand forested lands. This type of integrated land-use modeling can help ensure policy coherence in land and food systems across national strategic plans for climate, biodiversity, and agricultural self-sufficiency, each spearheaded by different government agencies. Importantly, a sensitivity analysis highlights the transformative impact that diets have on land-use systems, and as such, dietary transformation should be considered in all climate mitigation plans.
Published: 2023

42. Contributions of healthier diets and agricultural productivity toward sustainability and climate goals in the United States

Author: Wu, Grace C, Baker, Justin S, Wade, Christopher M, McCord, Gordon C, Fargione, Joseph E, and Havlik, Petr
Subjects: Climate Action, Life on Land, Decent Work and Economic Growth, Land use, Diets, Agriculture, GHG emissions, FABLE, Environmental Sciences
Abstract: Meeting ambitious climate targets will require deploying the full suite of mitigation options, including those that indirectly reduce greenhouse-gas (GHG) emissions. Healthy diets have sustainability co-benefits by directly reducing livestock emissions as well as indirectly reducing land use emissions. Increased crop productivity could indirectly avoid emissions by reducing cropland area. However, there is disagreement on the sustainability of proposed healthy U.S. diets and a lack of clarity on how long-term sustainability benefits may change in response to shifts in the livestock sector. Here, we explore the GHG emissions impacts of seven scenarios that vary U.S. crop yields and healthier diets in the U.S. and overseas. We also examine how impacts vary across assumptions of future ruminant livestock productivity and ruminant stocking density in the U.S. We employ two complementary land use models—the US FABLE Calculator, an agricultural and forestry sector accounting model with high agricultural commodity representation, and GLOBIOM, a spatially explicit partial equilibrium optimization model for global land use systems. Results suggest that healthier U.S. diets that follow the Dietary Guidelines for Americans reduce agricultural and land use greenhouse gas emissions by 25–57% (approx 120–310 MtCO2e/y) and pastureland area by 28–38%. The potential emissions and land sparing benefits of U.S. agricultural productivity growth are modest within the U.S. due to the increasing comparative advantage of U.S. crops. Our findings suggest that healthy U.S. diets can significantly contribute toward meeting U.S. long-term climate goals for the land use sectors.
Published: 2023

43. Rethinking Placemaking in Urban Planning Through the Lens of Trauma

Author: Douglas, Gordon C. C., primary
Published: 2024
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44. Bioactive Molecules of Medicinal Value in Marine Green Algae

Author: Rowaiye, Adekunle Babajide, primary, Morikwe, Ugonna, additional, Oni, Solomon, additional, Abakpa, Grace Onyukwo, additional, Okon, Itoroabasi Joseph, additional, Osisami, Olubukunola, additional, and Ibeanu, Gordon C., additional
Published: 2024
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45. Overview of the Instrumentation for the Dark Energy Spectroscopic Instrument

Author: Abareshi, B., Aguilar, J., Ahlen, S., Alam, Shadab, Alexander, David M., Alfarsy, R., Allen, L., Prieto, C. Allende, Alves, O., Ameel, J., Armengaud, E., Asorey, J., Aviles, Alejandro, Bailey, S., Balaguera-Antolínez, A., Ballester, O., Baltay, C., Bault, A., Beltran, S. F., Benavides, B., BenZvi, S., Berti, A., Besuner, R., Beutler, Florian, Bianchi, D., Blake, C., Blanc, P., Blum, R., Bolton, A., Bose, S., Bramall, D., Brieden, S., Brodzeller, A., Brooks, D., Brownewell, C., Buckley-Geer, E., Cahn, R. N., Cai, Z., Canning, R., Rosell, A. Carnero, Carton, P., Casas, R., Castander, F. J., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chuang, C., Circosta, C., Cole, S., Cooper, A. P., da Costa, L., Cousinou, M. -C., Cuceu, A., Davis, T. M., Dawson, K., de la Cruz-Noriega, R., de la Macorra, A., de Mattia, A., Della Costa, J., Demmer, P., Derwent, M., Dey, A., Dey, B., Dhungana, G., Ding, Z., Dobson, C., Doel, P., Donald-McCann, J., Donaldson, J., Douglass, K., Duan, Y., Dunlop, P., Edelstein, J., Eftekharzadeh, S., Eisenstein, D. J., Enriquez-Vargas, M., Escoffier, S., Evatt, M., Fagrelius, P., Fan, X., Fanning, K., Fawcett, V. A., Ferraro, S., Ereza, J., Flaugher, B., Font-Ribera, A., Forero-Romero, J. E., Frenk, C. S., Fromenteau, S., Gänsicke, B. T., Garcia-Quintero, C., Garrison, L., Gaztañaga, E., Gerardi, F., Gil-Marín, H., Gontcho, S. Gontcho A, Gonzalez-Morales, Alma X., Gonzalez-de-Rivera, G., Gonzalez-Perez, V., Gordon, C., Graur, O., Green, D., Grove, C., Gruen, D., Gutierrez, G., Guy, J., Hahn, C., Harris, S., Herrera, D., Herrera-Alcantar, Hiram K., Honscheid, K., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Jelinsky, P., Jiang, L., Jimenez, J., Jing, Y. P., Joyce, R., Jullo, E., Juneau, S., Karaçaylı, N. G., Karamanis, M., Karcher, A., Karim, T., Kehoe, R., Kent, S., Kirkby, D., Kisner, T., Kitaura, F., Koposov, S. E., Kovács, A., Kremin, A., Krolewski, Alex, L'Huillier, B., Lahav, O., Lambert, A., Lamman, C., Lan, Ting-Wen, Landriau, M., Lane, S., Lang, D., Lange, J. U., Lasker, J., Guillou, L. Le, Leauthaud, A., Van Suu, A. Le, Levi, Michael E., Li, T. S., Magneville, C., Manera, M., Manser, Christopher J., Marshall, B., McCollam, W., McDonald, P., Meisner, Aaron M., Mezcua, J. Mena-Fernández M., Miller, T., Miquel, R., Montero-Camacho, P., Moon, J., Martini, J. Paul, Meneses-Rizo, J., Moustakas, J., Mueller, E., Muñoz-Gutiérrez, Andrea, Myers, Adam D., Nadathur, S., Najita, J., Napolitano, L., Neilsen, E., Newman, Jeffrey A., Nie, J. D., Ning, Y., Niz, G., Norberg, P., Noriega, Hernán E., O'Brien, T., Obuljen, A., Palanque-Delabrouille, N., Palmese, A., Zhiwei, P., Pappalardo, D., Peng, X., Percival, W. J., Perruchot, S., Pogge, R., Poppett, C., Porredon, A., Prada, F., Prochaska, J., Pucha, R., Pérez-Fernández, A., Pérez-Ráfols, I., Rabinowitz, D., Raichoor, A., Ramirez-Solano, S., Ramírez-Pérez, César, Ravoux, C., Reil, K., Rezaie, M., Rocher, A., Rockosi, C., Roe, N. A., Roodman, A., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Sabiu, C. G., Safonova, S., Said, K., Saintonge, A., Catonga, Javier Salas, Samushia, L., Sanchez, E., Saulder, C., Schaan, E., Schlafly, E., Schlegel, D., Schmoll, J., Scholte, D., Schubnell, M., Secroun, A., Seo, H., Serrano, S., Sharples, Ray M., Sholl, Michael J., Silber, Joseph Harry, Silva, D. R., Sirk, M., Siudek, M., Smith, A., Sprayberry, D., Staten, R., Stupak, B., Tan, T., Tarlé, Gregory, Tie, Suk Sien, Tojeiro, R., Ureña-López, L. A., Valdes, F., Valenzuela, O., Valluri, M., Vargas-Magaña, M., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, C., Wechsler, R., Wilson, Michael J., Yang, J., Yu, Y., Yuan, S., Yèche, Christophe, Zhang, H., Zhang, K., Zhao, Cheng, Zhou, Rongpu, Zhou, Zhimin, Zou, H., Zou, J., Zou, S., and Zu, Y.
Subjects: Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract: The Dark Energy Spectroscopic Instrument (DESI) has embarked on an ambitious five-year survey to explore the nature of dark energy with spectroscopy of 40 million galaxies and quasars. DESI will determine precise redshifts and employ the Baryon Acoustic Oscillation method to measure distances from the nearby universe to z > 3.5, as well as measure the growth of structure and probe potential modifications to general relativity. In this paper we describe the significant instrumentation we developed for the DESI survey. The new instrumentation includes a wide-field, 3.2-deg diameter prime-focus corrector that focuses the light onto 5020 robotic fiber positioners on the 0.812 m diameter, aspheric focal surface. The positioners and their fibers are divided among ten wedge-shaped petals. Each petal is connected to one of ten spectrographs via a contiguous, high-efficiency, nearly 50 m fiber cable bundle. The ten spectrographs each use a pair of dichroics to split the light into three channels that together record the light from 360 - 980 nm with a resolution of 2000 to 5000. We describe the science requirements, technical requirements on the instrumentation, and management of the project. DESI was installed at the 4-m Mayall telescope at Kitt Peak, and we also describe the facility upgrades to prepare for DESI and the installation and functional verification process. DESI has achieved all of its performance goals, and the DESI survey began in May 2021. Some performance highlights include RMS positioner accuracy better than 0.1", SNR per \sqrt{\AA} > 0.5 for a z > 2 quasar with flux 0.28e-17 erg/s/cm^2/A at 380 nm in 4000s, and median SNR = 7 of the [OII] doublet at 8e-17 erg/s/cm^2 in a 1000s exposure for emission line galaxies at z = 1.4 - 1.6. We conclude with highlights from the on-sky validation and commissioning of the instrument, key successes, and lessons learned. (abridged), Comment: 78 pages, 32 figures, submitted to AJ
Published: 2022
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46. Extended panel testing in ovarian cancer reveals BRIP1 as the third most important predisposition gene

Author: Morgan, Robert D., Burghel, George J., Flaum, Nicola, Schlecht, Helene, Clamp, Andrew R., Hasan, Jurjees, Mitchell, Claire, Salih, Zena, Moon, Sarah, Hogg, Martin, Lord, Rosemary, Forde, Claire, Lalloo, Fiona, Woodward, Emma R., Crosbie, Emma J., Taylor, Stephen S., Jayson, Gordon C., and Evans, D. Gareth R.
Published: 2024
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47. Gut microbiota alteration - Cancer relationships and synbiotic roles in cancer therapies

Author: Rowaiye, Adekunle, Ibeanu, Gordon C., Bur, Doofan, Nnadi, Sandra, Mgbeke, Odinaka E., and Morikwe, Ugonna
Published: 2024
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48. Comparing survival rates and mortality in operative versus nonoperative treatment for femoral neck fractures among Alzheimer's disease patients: A retrospective cohort study

Author: Yijiong Yang, Stacy A. Drake, Jing Wang, Gordon C. Shen, Hongyu Miao, Robert O. Morgan, Xianglin L. Du, and David R. Lairson
Subjects: Alzheimer's disease and Alzheimer's disease related dementias, arthroplasty, femoral neck fracture, internal fixation, non‐operative treatment, Geriatrics, RC952-954.6
Abstract: Abstract Introduction Addressing femoral neck fractures resulting from ground‐level falls in older adults with Alzheimer's disease (AD) involves a personalized treatment plan. There is considerable ongoing debate concerning the relative advantages and disadvantages of surgical treatment (internal fixation or arthroplasty) vs nonoperative treatment for femoral neck fractures in older persons with AD. Methods This retrospective cohort study compared the mortality, hazard ratio, and survival rate between operative and nonoperative treatments, controlling for patients' demographic information and baseline health status. The study population consisted of Optum beneficiaries diagnosed with AD who experienced an initial femoral neck fracture claim between January 1, 2012, and December 31, 2017. Kaplan–Meier survival curves were applied to compare the treatment groups' post‐fracture survival rates and mortality. Cox regression was used to examine the survival period by controlling the covariates. Results Out of the 4157 patients with AD with femoral neck fractures, 59.8% were women (n = 2487). The median age was 81 years. The 1‐year survival rate for nonoperative treatment (70.19%) was lower than that for internal fixation (75.27%) and arthroplasty treatment (82.32%). Compared with the nonoperative group, arthroplasty surgical treatment had significant lower hazard risk of death (arthroplasty hazard ratio: 0.850, 95% CI: 0.728–0.991, P
Published: 2024
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49. An updated PREDICT breast cancer prognostic model including the benefits and harms of radiotherapy

Author: Isabelle Grootes, Gordon C. Wishart, and Paul David Peter Pharoah
Subjects: Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract: Abstract PREDICT Breast ( www.breast .predict.nhs.uk ) is a prognostication tool for early invasive breast cancer. The current version was based on cases diagnosed in 1999–2003 and did not incorporate the benefits of radiotherapy or the harms associated with therapy. Since then, there has been a substantial improvement in the outcomes for breast cancer cases. The aim of this study was to update PREDICT Breast to ensure that the underlying model is appropriate for contemporary patients. Data from the England National Cancer Registration and Advisory Service for invasive breast cancer cases diagnosed 2000–17 were used for model development and validation. Model development was based on 35,474 cases diagnosed and registered by the Eastern Cancer Registry. A Cox model was used to estimate the prognostic effects of the year of diagnosis, age at diagnosis, tumour size, tumour grade and number of positive nodes. Separate models were developed for ER-positive and ER-negative disease. Data on 32,408 cases from the West Midlands Cancer Registry and 100,551 cases from other cancer registries were used for validation. The new model was well-calibrated; predicted breast cancer deaths at 5-, 10- and 15-year were within 10 per cent of the observed validation data. Discrimination was also good: The AUC for 15-year breast cancer survival was 0.809 in the West Midlands data set and 0.846 in the data set for the other registries. The new PREDICT Breast model outperformed the current model and will be implemented in the online tool which should lead to more accurate absolute treatment benefit predictions for individual patients.
Published: 2024
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50. Cambios inducidos en nanotubos de carbono de capa única durante los procesos de purificación

Author: Martínez, M. T., Callejas, M. A., Benito, A. M., Cochet, M., Seeger, T., Ansón, A., Schreiber, J., Gordon, C., Marhic, C., Chauvet, O., and Maser, W. K.
Subjects: Nanotubes, Raman Spectroscopy, TEM, Nanotubos, espectroscopía Raman, microscopía de transmisión electrónica, Clay industries. Ceramics. Glass, TP785-869
Abstract: A systematic characterisation of single wall carbon nanotubes (SWCNTs) material after successive purification steps, including reflux treatment with nitric acid, air-oxidation and annealing, has been performed. During the nitric acid reflux treatment, micro Raman spectroscopy further proves that the SWCNTs diameter distribution can be selectively tuned towards smaller tubes. On the other hand, the subsequent oxidation/ annealing processes lead to samples preferentially containing larger tube diameter. These findings are further underlined by transmission electron microscopy. The applied purification process efficiently removes the undesired species of metal nanoparticles and amorphous carbon thus resulting in a high quality SWCNTs material.Se ha llevado a cabo una caracterización sistemática de nanotubos de carbono de capa única tras sucesivos pasos de purificación (tratamiento a reflujo con ácido nítrico, oxidación al aire y anelado). Durante el tratamiento a reflujo con ácido nítrico, la espectroscopía Raman reveló un desplazamiento de la distribución de diámetros de los nanotubos hacia tamaños menores, sin embargo, los procesos siguientes de oxidación y de anelado aumentaron el contenido de nanotubos de mayor diámetro. La morfología de los haces de nanotubos caracterizada por microscopía electrónica de transmisión ha mostrado un aumento del tamaño de los mismos. Los procesos de purificación aplicados han originado un material con nanotubos de carbono de capa única de alta calidad, con una importante reducción de especies no deseadas tales como carbono amorfo y nanopartículas metálicas.
Published: 2004

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